Automated species identification is a method of making the expertise of
taxonomists
In biology, taxonomy () is the scientific study of naming, defining ( circumscribing) and classifying groups of biological organisms based on shared characteristics. Organisms are grouped into taxa (singular: taxon) and these groups are given ...
available to ecologists,
parataxonomists and others via digital technology and
artificial intelligence
Artificial intelligence (AI) is intelligence—perceiving, synthesizing, and inferring information—demonstrated by machines, as opposed to intelligence displayed by animals and humans. Example tasks in which this is done include speech re ...
. Today, most automated identification systems rely on images depicting the species for the identification. Based on precisely identified images of a species, a
classifier is trained. Once exposed to a sufficient amount of training data, this classifier can then identify the trained species on previously unseen images.
Introduction
The automated identification of biological objects such as
insects
Insects (from Latin ') are pancrustacean hexapod invertebrates of the class Insecta. They are the largest group within the arthropod phylum. Insects have a chitinous exoskeleton, a three-part body (head, thorax and abdomen), three pairs of j ...
(individuals) and/or groups (e.g.,
species
In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriate s ...
, guilds, characters) has been a dream among
systematists
Biological systematics is the study of the diversification of living forms, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees (synonyms: cladograms, phylogenetic tr ...
for centuries. The goal of some of the first
multivariate
Multivariate may refer to:
In mathematics
* Multivariable calculus
* Multivariate function
* Multivariate polynomial
In computing
* Multivariate cryptography
* Multivariate division algorithm
* Multivariate interpolation
* Multivariate optical c ...
biometric
Biometrics are body measurements and calculations related to human characteristics. Biometric authentication (or realistic authentication) is used in computer science as a form of identification and access control. It is also used to identify in ...
methods was to address the perennial problem of
group discrimination and inter-group characterization. Despite much preliminary work in the 1950s and '60s, progress in designing and implementing practical systems for fully automated object biological
identification
Identification or identify may refer to:
*Identity document, any document used to verify a person's identity
Arts, entertainment and media
* ''Identify'' (album) by Got7, 2014
* "Identify" (song), by Natalie Imbruglia, 1999
* Identification ( ...
has proven frustratingly slow. As recently as 2004
Dan Janzen
updated the dream for a new audience:
The spaceship lands. He steps out. He points it around. It says 'friendly–unfriendly—edible–poisonous—safe– dangerous—living–inanimate'. On the next sweep it says Quercus oleoides—Homo sapiens—Spondias mombin—Solanum nigrum—Crotalus durissus—Morpho peleides''—serpentine'. This has been in my head since reading science fiction in ninth grade half a century ago.
The species identification problem
Janzen's preferred solution to this classic problem involved building machines to identify species from their
DNA. However, recent developments in computer architectures, as well as innovations in software design, have placed the tools needed to realize Janzen's vision in the hands of the
systematics
Biological systematics is the study of the diversification of living forms, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees (synonyms: cladograms, phylogenetic tre ...
and
computer science
Computer science is the study of computation, automation, and information. Computer science spans theoretical disciplines (such as algorithms, theory of computation, information theory, and automation) to Applied science, practical discipli ...
community not in several years hence, but now; and not just for creating
DNA barcode
DNA barcoding is a method of species identification using a short section of DNA from a specific gene or genes. The premise of DNA barcoding is that by comparison with a reference library of such DNA sections (also called "sequences"), an indiv ...
s, but also for identification based on
digital images
A digital image is an image composed of picture elements, also known as ''pixels'', each with ''finite'', '' discrete quantities'' of numeric representation for its intensity or gray level that is an output from its two-dimensional functions f ...
.
A survey published in 2004, studies why automated species identification had not become widely employed at this time and whether it would be a realistic option for the future. The authors found that "a small but growing number of studies sought to develop automated species identification systems based on morphological characters". An overview of 20 studies analyzing species' structures, such as cells, pollen, wings, and genitalia, shows identification success rates between 40% and 100% on training sets with 1 to 72 species. However, they also identified four fundamental problems with these systems: (1) training sets—were too small (5-10 specimens per species) and their extension especially for rare species may be difficult, (2) errors in identification—are not sufficiently studied to handle them and to find systematics, (3) scaling—studies consider only small numbers of species (<200 species), and (4) novel species — systems are restricted to the species they have been trained for and will classify any novel observation as one of the known species.
A survey published in 2017 systematically compares and discusses progress and findings towards automated plant species identification within the last decade (2005–2015). 120 primary studies have been published in high-quality venues within this time, mainly by authors with computer science background. These studies propose a wealth of
computer vision
Computer vision is an interdisciplinary scientific field that deals with how computers can gain high-level understanding from digital images or videos. From the perspective of engineering, it seeks to understand and automate tasks that the hum ...
approaches, i.e.,
features
Feature may refer to:
Computing
* Feature (CAD), could be a hole, pocket, or notch
* Feature (computer vision), could be an edge, corner or blob
* Feature (software design) is an intentional distinguishing characteristic of a software item ...
reducing the high-dimensionality of the pixel-based image data while preserving the characteristic information as well as classification methods. The vast majority of these studies analyzes
leaves
A leaf (plural, : leaves) is any of the principal appendages of a vascular plant plant stem, stem, usually borne laterally aboveground and specialized for photosynthesis. Leaves are collectively called foliage, as in "autumn foliage", wh ...
for identification, while only 13 studies propose methods for
flower
A flower, sometimes known as a bloom or blossom, is the reproductive structure found in flowering plants (plants of the division Angiospermae). The biological function of a flower is to facilitate reproduction, usually by providing a mechani ...
-based identification. The reasons being that leaves can easier be collected and imaged and are available for most of the year. Proposed
features
Feature may refer to:
Computing
* Feature (CAD), could be a hole, pocket, or notch
* Feature (computer vision), could be an edge, corner or blob
* Feature (software design) is an intentional distinguishing characteristic of a software item ...
capture generic object characteristic, i.e.,
shape
A shape or figure is a graphics, graphical representation of an object or its external boundary, outline, or external Surface (mathematics), surface, as opposed to other properties such as color, Surface texture, texture, or material type.
A pl ...
, texture, and
color
Color (American English) or colour (British English) is the visual perceptual property deriving from the spectrum of light interacting with the photoreceptor cells of the eyes. Color categories and physical specifications of color are associ ...
as well as leaf-specific characteristics, i.e.,
venation
Venation may refer to:
* Venation (botany), the arrangement of veins in leaves
* Wing venation, the arrangement of veins in insect wings
See also
*
* Vernation
Vernation (from ''vernal'' meaning ''spring'', since that is when leaves spring forth ...
and margin. The majority of studies still used datasets for evaluation that contained no more than 250
species
In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriate s ...
. However, there is progress in this regard, one study uses a dataset with >2k and another with >20k
species
In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriate s ...
.
A system developed in 2022 showed that automated identification achieves accuracy that is sufficiently high for being used in an automated insect surveillance system using electronic traps. By training classifiers on a few hundred images it correctly identified fruit-flies, and can be used for continuous monitoring aimed at detecting species invasion or pest outbreak. Several aspects contribute to the success of this system. Primarily, using e-traps provide a standardized setting, which means that even though they are deployed in different countries and regions, the visual variability, in terms of size view angle and illumination are controlled. This suggests that trap-based systems may be easier to develop than free-view systems for automatic pest identification.
There is a shortage of specialists who can identify the very
biodiversity
Biodiversity or biological diversity is the variety and variability of life on Earth. Biodiversity is a measure of variation at the genetic (''genetic variability''), species (''species diversity''), and ecosystem (''ecosystem diversity'') l ...
whose preservation has become a global concern. In commenting on this problem in
palaeontology
Paleontology (), also spelled palaeontology or palæontology, is the scientific study of life that existed prior to, and sometimes including, the start of the Holocene epoch (roughly 11,700 years before present). It includes the study of fossi ...
in 1993,
Roger Kaesler
Roger is a given name, usually masculine, and a surname. The given name is derived from the Old French personal names ' and '. These names are of Germanic origin, derived from the elements ', ''χrōþi'' ("fame", "renown", "honour") and ', ' ( ...
recognized:
"... we are running out of systematic palaeontologists who have anything approaching synoptic knowledge of a major group of organisms ... Palaeontologists of the next century are unlikely to have the luxury of dealing at length with taxonomic problems ... Palaeontology will have to sustain its level of excitement without the aid of systematists, who have contributed so much to its success."
This expertise deficiency cuts as deeply into those commercial industries that rely on accurate identifications (e.g.,
agriculture
Agriculture or farming is the practice of cultivating plants and livestock. Agriculture was the key development in the rise of sedentary human civilization, whereby farming of domesticated species created food surpluses that enabled people to ...
,
biostratigraphy
Biostratigraphy is the branch of stratigraphy which focuses on correlating and assigning relative ages of rock Stratum, strata by using the fossil assemblages contained within them.Hine, Robert. “Biostratigraphy.” ''Oxford Reference: Dictiona ...
) as it does into a wide range of pure and applied research programmes (e.g.,
conservation
Conservation is the preservation or efficient use of resources, or the conservation of various quantities under physical laws.
Conservation may also refer to:
Environment and natural resources
* Nature conservation, the protection and manageme ...
, biological
oceanography
Oceanography (), also known as oceanology and ocean science, is the scientific study of the oceans. It is an Earth science, which covers a wide range of topics, including ecosystem dynamics; ocean currents, waves, and geophysical fluid dynamic ...
,
climatology
Climatology (from Greek , ''klima'', "place, zone"; and , '' -logia'') or climate science is the scientific study of Earth's climate, typically defined as weather conditions averaged over a period of at least 30 years. This modern field of stud ...
,
ecology
Ecology () is the study of the relationships between living organisms, including humans, and their physical environment. Ecology considers organisms at the individual, population, community, ecosystem, and biosphere level. Ecology overlaps wi ...
). It is also commonly, though informally, acknowledged that the technical, taxonomic literature of all organismal groups is littered with examples of inconsistent and incorrect identifications. This is due to a variety of factors, including taxonomists being insufficiently trained and skilled in making identifications (e.g., using different rules-of-thumb in recognizing the boundaries between similar groups), insufficiently detailed original group descriptions and/or illustrations, inadequate access to current monographs and well-curated collections and, of course, taxonomists having different opinions regarding group concepts. Peer review only weeds out the most obvious errors of commission or omission in this area, and then only when an author provides adequate representations (e.g., illustrations, recordings, and gene sequences) of the specimens in question.
Systematics
Biological systematics is the study of the diversification of living forms, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees (synonyms: cladograms, phylogenetic tre ...
too has much to gain from the further development and use of automated identification systems. In order to attract both personnel and resources, systematics must transform itself into a "large, coordinated, international scientific enterprise".
Many have identified use of the
Internet
The Internet (or internet) is the global system of interconnected computer networks that uses the Internet protocol suite (TCP/IP) to communicate between networks and devices. It is a '' network of networks'' that consists of private, pub ...
— especially via the
World Wide Web
The World Wide Web (WWW), commonly known as the Web, is an information system enabling documents and other web resources to be accessed over the Internet.
Documents and downloadable media are made available to the network through web se ...
— as the medium through which this transformation can be made. While establishment of a virtual,
GenBank
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a part ...
-like system for accessing
morphological data, audio clips, video files and so forth would be a significant step in the right direction, improved access to observational information and/or text-based descriptions alone will not address either the
taxonomic impediment or low identification reproducibility issues successfully. Instead, the inevitable subjectivity associated with making critical decisions on the basis of qualitative criteria must be reduced or, at the very least, embedded within a more formally analytic context.
Properly designed, flexible, and robust, automated identification systems, organized around distributed computing architectures and referenced to authoritatively identified collections of training set data (e.g., images, and
gene sequence
In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...
s) can, in principle, provide all systematists with access to the electronic data archives and the necessary analytic tools to handle routine identifications of common taxa. Properly designed systems can also recognize when their algorithms cannot make a reliable identification and refer that image to a specialist (whose address can be accessed from another database). Such systems can also include elements of artificial intelligence and so improve their performance the more they are used. Once morphological (or molecular) models of a species have been developed and demonstrated to be accurate, these models can be queried to determine which aspects of the observed patterns of variation and variation limits are being used to achieve the identification, thus opening the way for the discovery of new and (potentially) more reliable taxonomic characters.
*
iNaturalist
iNaturalist is a social network of naturalists, citizen scientists, and biologists built on the concept of mapping and sharing observations of biodiversity across the globe. iNaturalist may be accessed via its website or from its mobile applic ...
is a global citizen science project and social network of naturalists that incorporates both human and automatic identification of plants, animals, and other living creatures via browser or mobile apps.
*
Pl@ntNet
Pl@ntNet is a citizen science project for automatic plant identification through photographs and based on machine learning.
History
This project launched in 2009 has been developed by scientists ( computer engineers and botanists) from a co ...
is a global citizen science project which provides an app and a website for plant identification through photographs, based on machine-learning
*
Leaf Snap
A leaf (plural, : leaves) is any of the principal appendages of a vascular plant plant stem, stem, usually borne laterally aboveground and specialized for photosynthesis. Leaves are collectively called foliage, as in "autumn foliage", wh ...
is an iOS app developed by the
Smithsonian Institution
The Smithsonian Institution ( ), or simply the Smithsonian, is a group of museums and education and research centers, the largest such complex in the world, created by the U.S. government "for the increase and diffusion of knowledge". Founded ...
that uses visual recognition software to identify North American tree species from photographs of leaves.
*
Google Photos
Google Photos is a photo sharing and storage service developed by Google. It was announced in May 2015 and spun off from Google+, the company's former social network.
As of June 1, 2021, in its free tier, any newly uploaded photo and video c ...
can automatically identify various species in photographs.
*
Plant.id is a web application and
API
An application programming interface (API) is a way for two or more computer programs to communicate with each other. It is a type of software Interface (computing), interface, offering a service to other pieces of software. A document or standa ...
made by
FlowerChecker company which uses a neural network trained on photos from FlowerChecker mobile app.
See also
*
Multi-access key In biology or medicine, a multi-access key is an identification key which overcomes the problem of the more traditional single-access key
In phylogenetics, a single-access key (also called dichotomous key, sequential key, analytical key, or pathway ...
References cited
External links
Here are some links to the home pages of species identification systems. The SPIDA and
DAISY system are essentially generic and capable of classifying any image material presented. The ABIS and DrawWing system are restricted to insects with membranous wings as they operate by matching a specific set of characters based on wing venation.
The SPIDA systemABISDAISYDrawWingLeafSnapPl@ntNet
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Species
Automatic identification and data capture
Comparative anatomy
Bioinformatics
Applications of computer vision